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Bacterial Chondronecrosis With Osteomyelitis In Broilers: Genomics, Phylogenomics, And Methods To Detect Specific Pathogens During Outbreaks., Abdulkarim Abdulaziz A. Shwani 2022 University of Arkansas, Fayetteville

Bacterial Chondronecrosis With Osteomyelitis In Broilers: Genomics, Phylogenomics, And Methods To Detect Specific Pathogens During Outbreaks., Abdulkarim Abdulaziz A. Shwani

Graduate Theses and Dissertations

Lameness is a major issue in animal welfare and the broiler industry. Bacterial chondronecrosis with osteomyelitis (BCO) is one of the main causes of lameness. Many staphylococcal species, including Staphylococcus agnetis isolate 908, have been isolated from the bones and blood of lame broilers at the University of Arkansas. Staphylococcus agnetis is a coagulase-variable, Gram-positive bacterial species that has been previously associated with subclinical or mild clinical cases of mastitis in dairy cattle. The annotated complete genome of hypervirulent strain 908 was published at NCBI. In this study, it has been compared to nine genomes we assembled for hypervirulent isolates ...


Allelopathic Effect Of Cereal Straw Extracts On Growth Of Raphidocelis Subcapitata And Microcystis Aeruginosa, Holly Wren 2022 University of Arkansas, Fayetteville

Allelopathic Effect Of Cereal Straw Extracts On Growth Of Raphidocelis Subcapitata And Microcystis Aeruginosa, Holly Wren

Graduate Theses and Dissertations

Harmful algal blooms are increasing in size, duration, and intensity around the globe. For several decades, cereal straws have been recognized as a viable algal control method, though the mechanisms by which cereal straws inhibit algae remain a topic of research. The objectives of this study were to evaluate the effectiveness of decomposing cereal straw extract, particularly rice (Oryza sativa) and barley (Hordeum vulgare) straw extract, to inhibit the green alga Raphidocelis subcapitata or cyanobacteria Microcystis aeruginosa in bioassays and to determine if the effectiveness of decomposing rice straw extract is altered by the presence of natural organic matter or ...


Weaving An Interdisciplinary Microbiome Career Using Threads From Different Ecosystems, Sarah Hosler 2022 University of Maine

Weaving An Interdisciplinary Microbiome Career Using Threads From Different Ecosystems, Sarah Hosler

Electronic Theses and Dissertations

Animals have trillions of microorganisms living in or on many body sites, these communities of microorganisms are called microbiomes. Microbiomes are typically host-specific, and a lot of information about the host can be determined from investigating them. Microbiome research has many real-world applications, and this thesis utilizes the One Health perspective, which acknowledges the connection of humans, animals, and environments, and emphasizes the need for collaborative, interdisciplinary research. The first interdisciplinary project is an investigation into the bacteria in wild and cultured Atlantic deep-sea scallop, Placopecten magellanicus larvae. Adults in hatcheries can be induced to spawn, but the last two ...


An Overview Of The Extracurricular Polysaccaride Production Of Probiotic Lactic Acid Bacteria, Olujimi Babajide Olowokere 2022 Texas Southern University

An Overview Of The Extracurricular Polysaccaride Production Of Probiotic Lactic Acid Bacteria, Olujimi Babajide Olowokere

Theses (2016-Present)

The study focuses on a comprehensive review of lactic acid bacteria and their production of extracellular polysaccharide substrates (EPS). Two important factors are addressed in the work; and these are 1) identification of LAB stains found in the commercially sold daily milk, 2) significant factors impacting polysaccharide production. Motivation behind these focus points is to allow further inquiries and studies on exploring these strains of bacteria for human wellness promotion. With microbial EPS production being a recent interest of study among healthcare and food industries sectors, new species of bacteria are extensively exploited for further investigation to improve human health ...


Defining The Importance Of The Hnrnp I Interaction To The Sindbis Virus Subgenomic Viral Rna Using An Innovative Tethering Approach., Claire Westcott 2022 University of Louisville

Defining The Importance Of The Hnrnp I Interaction To The Sindbis Virus Subgenomic Viral Rna Using An Innovative Tethering Approach., Claire Westcott

Electronic Theses and Dissertations

Old World alphaviruses cause significant outbreaks of illness and debilitating multi-joint arthritis for prolonged periods. Currently, there are no FDA approved vaccines or antiviral therapies; and thus, there is a critical need to identify and characterize the molecular biology of alphaviruses. Alphaviruses rely on the host cell machinery to complete the viral lifecycle and are dependent on interactions with host RNA binding proteins. Accordingly, several host heterogenous nuclear ribonucleoprotein proteins (hnRNPs) have been found to bind to the Sindbis virus (SINV) RNAs. Disrupting the interaction sites in the viral RNAs of these RNA:Protein interactions results in decreased viral titers ...


Clostridioides Difficile Biofilm And Spore Production In Response To Antibiotics And Immune Stress, Adenrele M. Oludiran 2022 Old Dominion University

Clostridioides Difficile Biofilm And Spore Production In Response To Antibiotics And Immune Stress, Adenrele M. Oludiran

Chemistry & Biochemistry Theses & Dissertations

The development of new therapeutic options against Clostridioides difficile (C. difficile) infection is a critical public health concern, as the causative bacterium is highly resistant to multiple classes of antibiotics. C. difficile, an anaerobic spore-forming Gram-positive pathogenic bacterium, is a major cause of hospital-acquired infections. C. difficile persists in the environment and spreads the infection to new hosts in the form of dormant spores and can persist within hosts as surface-attached biofilms. These studies investigate bacterial vegetative cell survival, biofilm formation, and sporulation in response to stress. Antimicrobial host-defense peptides (HDPs) are highly effective at simultaneously modulating immune system function ...


Microbial, Chemical, And Functional Components In Kefir, Natto, And Feed Ingredients, Dana McCurdy 2022 Clemson University

Microbial, Chemical, And Functional Components In Kefir, Natto, And Feed Ingredients, Dana Mccurdy

All Dissertations

Kefir grains were purchased from online, home kitchen vendors in the United States (n = 22), inoculated into UHT milk, and incubated at 25°C for 22 hours. Results indicated lactobacilli, lactococci and yeast in all samples. Six out of 11 samples contained coliform, and all samples contained pseudomonal and staphylococcal species. Using targeted genome sequencing (16S) of kefir grain samples 1, 2, and 3 revealed that lactobacilli were the predominant genera of bacteria. ITS sequencing revealed different fungal species in each grain. Results indicated potential presence of menaquinone-4 and menaquinone-7 by UPLC-MS/MS analysis.

The fermentation of whole and ground ...


Exploring Microbes At Wind Cave As An Analog For Exobiological Environments Off Earth, Abby K. Sliwiniski, Emma W. Pellegrino, Nicole Geerdes, Marek K. Sliwinski 2022 University of Northern Iowa

Exploring Microbes At Wind Cave As An Analog For Exobiological Environments Off Earth, Abby K. Sliwiniski, Emma W. Pellegrino, Nicole Geerdes, Marek K. Sliwinski

Summer Undergraduate Research Program (SURP) Symposium

Subterranean environments on Earth serve as an analog for the study of microbes on other planets. This has become an active area of research with the discovery of exoplanets. To learn about the microbial species living in Wind Cave, we are comparing methods to sample environmental DNA because most microbes cannot be cultivated using standard laboratory methods. We are then probing the environmental DNA with broad primers that are designed to amplify most life and narrower primers such as those specific to the domain Archaea. Of the methods compared, the Qiagen DNeasy Powerbiofilm kit produced the purest template as measured ...


Arsr Family Regulator Msmeg_6762 Mediates The Programmed Cell Death By Regulating The Expression Of Hnh Nuclease In Mycobacteria, Xiangke Duan, Xue Huang, Junqi Xu, Xue Li, Jingjing Niu, Xiaoli Du, Xiaoyu Wang, Jiang Li, Michael Kelly, Jiaohan Guo, Ke Zhang, Yu Huang, Biao Kan, Jianping Xie 2022 College of Saint Benedict/Saint John's University

Arsr Family Regulator Msmeg_6762 Mediates The Programmed Cell Death By Regulating The Expression Of Hnh Nuclease In Mycobacteria, Xiangke Duan, Xue Huang, Junqi Xu, Xue Li, Jingjing Niu, Xiaoli Du, Xiaoyu Wang, Jiang Li, Michael Kelly, Jiaohan Guo, Ke Zhang, Yu Huang, Biao Kan, Jianping Xie

Biology Student Work

Programmed cell death (PCD) is the result of an intracellular program and is accomplished by a regulated process in both prokaryotic and eukaryotic organisms. Here, we report a programed cell death process in Mycobacterium smegmatis, an Actinobacteria species which involves a transcription factor and a DNase of the HNH family. We found that over-expression of an ArsR family member of the transcription factor, MSMEG_6762, leads to cell death. Transcriptome analysis revealed an increase in the genes’ transcripts involved in DNA repair and homologous recombination, and in three members of HNH family DNases. Knockout of one of the DNase genes, MSMEG_1275 ...


Regulation Of Mhc Ii Trafficking And Expression By Host And Viral Factors, Alex Lac 2022 The University of Western Ontario

Regulation Of Mhc Ii Trafficking And Expression By Host And Viral Factors, Alex Lac

Electronic Thesis and Dissertation Repository

Antigen presentation by major histocompatibility complex class II (MHC II) to the adaptive immune system is crucial for mounting sterilizing immune responses. This central role has made antigen presentation a target for antagonism by many pathogens. Notably, infections with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) decrease MHC II expression in several immune cells. The mechanisms responsible for this suppression are unknown but involves either redirecting MHC II molecules away from the cell surface or inhibiting MHC II expression. To understand how pathogens manipulate intracellular MHC II trafficking, we first investigated the role of the Golgi trafficking regulator, ERC1, in ...


Discovering Novel Polyextremotolerant Fungi, And Determining Their Ecological Role Within The Biological Soil Crust Consortium, Erin Carr 2022 University of Nebraska-Lincoln

Discovering Novel Polyextremotolerant Fungi, And Determining Their Ecological Role Within The Biological Soil Crust Consortium, Erin Carr

Dissertations and Theses in Biological Sciences

The ecological niche of polyextremotolerant fungi within oligotrophic ecosystems such as biological soil crusts has not yet been determined. These fungi persist in locations where nutrients are depleted while simultaneously surrounded by autotrophic microbes such as algae and cyanobacteria. Yet it has not been shown that they are engaging in any exchange of nutrients the way lichens do. However, there is seemingly no other way for these fungi to obtain vital nutrients, such as carbon or nitrogen, other than from these microbes. Here we have isolated polyextremotolerant fungi from cold desert biological soil crusts which are a microbial biofilm that ...


Analysis Of Geographic Variability Of Fecal Microbiomes Of Fratercula Arctica And Cross-Comparison Of Fecal Microbiomes Of Different Avian Feeding Types, Eric Jose Ramon Martinez 2022 Louisiana State University and Agricultural and Mechanical College

Analysis Of Geographic Variability Of Fecal Microbiomes Of Fratercula Arctica And Cross-Comparison Of Fecal Microbiomes Of Different Avian Feeding Types, Eric Jose Ramon Martinez

LSU Master's Theses

Gastrointestinal (gut) microbiota have a multitude of effects on their host, from aiding in digestion, to facilitating nutrient uptake, detoxification, and interactions with the immune system. Multiple factors have been identified that influence the composition of vertebrate microbiomes; these include host genetics, environmental conditions, diet and age, sex, and geography. However, broad inferences about wild avian gut microbial diversity and function under natural conditions are limited. Most knowledge on avian microbiomes is derived from studies on domestic poultry. Information on non-model taxa may provide important contextual information about vertebrate host-microbiome interactions and aid in future management of vulnerable species. Here ...


Molecular Mechanisms Underlying Mucosal Attachment And Colonization By Clostridioides Difficile, Ben Sidner 2022 University of Nebraska-Lincoln

Molecular Mechanisms Underlying Mucosal Attachment And Colonization By Clostridioides Difficile, Ben Sidner

Dissertations, Theses, & Student Research in Food Science and Technology

Clostridioides difficile is a Gram-positive, spore-forming, anaerobic bacterium which causes gastrointestinal disease and is a leading cause of nosocomial infections. Although infection typically occurs following antibiotic therapy, in recent years there has been an increase in infections which are not preceded by antibiotic use. Additionally, community-associated infections and rates of disease recurrence have increased. While it is understood that a healthy gastrointestinal microbiota provides protection against infection, the molecular mechanisms which underly C. difficile's ability to colonize and persist in the gut are mostly unknown. Building on work from others that suggests C. difficile associates with the outer mucus ...


Methanogen Metabolic Flexibility, Sean Carr 2022 University of Nebraska-Lincoln

Methanogen Metabolic Flexibility, Sean Carr

Dissertations and Theses in Biological Sciences

Methanogens are obligately anaerobic archaea which produce methane as a byproduct of their respiration. They are found across a wide diversity of environments and play an important role in cycling carbon in anaerobic spaces and the removal of harmful fermentation byproducts which would otherwise inhibit other organisms. Methanogens subsist on low-energy substrates which requires them to utilize a highly efficient central metabolism which greatly favors respiratory byproducts over biomass. This metabolic strategy creates high substrate:product conversion ratios which is industrially relevant for the production of biomethane, but may also allow for the production of value-added commodities. Particularly of interest ...


Tissue Decay Tested In Modern Metasequoia Leaves: Implications For Early Diagenesis Of Leaves In Fossil Lagerstätten, Caitlyn R. Witkowski, Qin Leng, Christopher W. Reid, Liang Feng, Hong Yang 2022 Bryant University

Tissue Decay Tested In Modern Metasequoia Leaves: Implications For Early Diagenesis Of Leaves In Fossil Lagerstätten, Caitlyn R. Witkowski, Qin Leng, Christopher W. Reid, Liang Feng, Hong Yang

Science and Technology Faculty Journal Articles

Sedimentary deposits yielding extraordinarily-preserved fossils (known as Lagerstätten) may provide significant insights into the physiology and environments of ancient plants, particularly when the fossils represent their original characteristics with limited diagenetic modifications. To better understand molecular, isotopic, and morphological changes during the early stages of diagenesis, degradation experiments were conducted in two time series: 1) a laboratory decay series using fungi on leaves over the course of a month and 2) a natural decay series with leaves collected from different stages of leaf senescence and early diagenesis. Both experiments used modern leaves of the dawn redwood Metasequoia glyptostroboides, referred to ...


Effects Of Surface Topography On Macrophages And Bacterial Cells, Joseph Carnicelli 2022 Syracuse University

Effects Of Surface Topography On Macrophages And Bacterial Cells, Joseph Carnicelli

Theses - ALL

An association has been found between the texture of breast implants and anaplastic large cell lymphoma, which led to some textured implants to be withdrawn from the market in 2019. There is evidence that these cancers are associated with the harboring of bacteria on the surfaces of the textured implants. It is possible that specific topographic features hinder the removal of attached bacteria by inhibiting macrophage phagocytosis or promoting biofilm formation. Here we examine how bacteria and macrophages interact with recessive surface topographies as analogs to the surfaces seen on textured breast implants. Changes in bacteria morphology were observed among ...


Jatropha Tanjorensis A Flora Of Southeast Nigeria: Isolation And Characterization Of Naringenin And Validation Of Bio-Enhanced Synergistical Activity Of Α- Tocopherol Toward Clinical Isolates Of Resistant Bacterial, Ikechukwu Kingsley Ijoma, Vincent Ishmael Egbulefu Ajiwe 2022 Nnamdi Azikiwe University, Awka, Anambra State 420007, Nigeria

Jatropha Tanjorensis A Flora Of Southeast Nigeria: Isolation And Characterization Of Naringenin And Validation Of Bio-Enhanced Synergistical Activity Of Α- Tocopherol Toward Clinical Isolates Of Resistant Bacterial, Ikechukwu Kingsley Ijoma, Vincent Ishmael Egbulefu Ajiwe

Makara Journal of Science

Jatropha tanjorensis is among the rich floras of Southeast Nigeria and used by ethnic people to treat infections and manage health conditions. Ethnomedicine has long been employed in the treatment of ailments caused by bacterial pathogens. Studies showed that the incorporation of synthetic α-tocopherol to an antibacterial agent improves its activity. However, knowledge about the antibacterial-enhanced activity of plant-based α-tocopherols, especially those isolated from Jatropha tanjorensis, is limited because of the different bioactivities of synthetic and natural α-tocopherols. To determine the phytochemicals in J. tanjorensis, we carried out the structural elucidation of its leaf extracts. Naringenin and α-tocopherol were identified ...


Molecular Identification Of Cryptococcus Neoformans Isolates From House Environments Of Hiv-Infected Patients In An Urban Area, Indonesia: A First Report, Machrumnizar Machrumnizar, Robiatul Adawiyah, Tjahjani Natriana, Darma Imran, Mohammad Muslim, Sjamsuridzal Wellyzar, Retno Wahyuningsih 2022 Magister Programme of Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jakarta 10440, Indonesia

Molecular Identification Of Cryptococcus Neoformans Isolates From House Environments Of Hiv-Infected Patients In An Urban Area, Indonesia: A First Report, Machrumnizar Machrumnizar, Robiatul Adawiyah, Tjahjani Natriana, Darma Imran, Mohammad Muslim, Sjamsuridzal Wellyzar, Retno Wahyuningsih

Makara Journal of Science

Cryptococcus neoformans isolates were previously obtained from pigeon droppings in Jakarta. This study aimed to determine another source of infection and describe the supporting niche of the fungus. The occurrence of C. neoformans was evaluated in 110 samples of decaying wood and leaves, tree hollow debris, dust, and bird droppings. Yeasts isolates were collected from 22 houses of HIV-infected patients. The isolates were identified based on culture characteristics, an assimilation test, and URA5 restriction fragment length polymorphism polymerase chain reaction. The spatial analysis was conducted in geographical information system to determine dominant house and environmental factors. Seven of the 120 ...


Increasing The Resilience Of Plant Immunity To A Warming Climate, Jong Hum Kim, Christian Castroverde, Shuai Huang, Chao Li, Richard Hilleary, Adam Seroka, Reza Sohrabi, Diana Medina-Yerena, Bethany Huot, Jie Wang, Sharon Marr, Mary Wildermuth, Tao Chen, John MacMicking, Sheng Yang He 2022 Duke University

Increasing The Resilience Of Plant Immunity To A Warming Climate, Jong Hum Kim, Christian Castroverde, Shuai Huang, Chao Li, Richard Hilleary, Adam Seroka, Reza Sohrabi, Diana Medina-Yerena, Bethany Huot, Jie Wang, Sharon Marr, Mary Wildermuth, Tao Chen, John Macmicking, Sheng Yang He

Biology Faculty Publications

Extreme weather conditions associated with climate change affect many aspects of plant and animal life, including the response to infectious diseases. Production of salicylic acid (SA), a central plant defence hormone, is particularly vulnerable to suppression by short periods of hot weather above the normal plant growth temperature range via an unknown mechanism. Here we show that suppression of SA production in Arabidopsis thaliana at 28 °C is independent of PHYTOCHROME B (phyB) and EARLY FLOWERING 3 (ELF3), which regulate thermo-responsive plant growth and development. Instead, we found that formation of GUANYLATE BINDING PROTEIN-LIKE 3 (GBPL3) defence-activated biomolecular condensates (GDACs ...


Presence Of Blaper-1 And Blaveb-1 Beta-Lactamase Genes Among Isolates Of Pseudomonas Aeruginosa From Burn And Trauma Hospital Peshawar, Pakistan, Suleman khan, Samiyah Tasleem, AlFarah Rehmat ullah,, Sarwat Moon, Saad Alghamdi, Raina Saad Suliman, Muhammad Ateeq, Muhmmad Salman, Anas S. Dablool,, Banan Atwah, Farkad Bantun 2022 Department of Health and Biological Sciences Abasyn University Peshawar, Pakistan.

Presence Of Blaper-1 And Blaveb-1 Beta-Lactamase Genes Among Isolates Of Pseudomonas Aeruginosa From Burn And Trauma Hospital Peshawar, Pakistan, Suleman Khan, Samiyah Tasleem, Alfarah Rehmat Ullah,, Sarwat Moon, Saad Alghamdi, Raina Saad Suliman, Muhammad Ateeq, Muhmmad Salman, Anas S. Dablool,, Banan Atwah, Farkad Bantun

Journal of Bioresource Management

Pseudomonas aeruginosa spp are the most prevalent bacteria that cause nosocomial infections in hospitals. Most antibiotics, including novel new β-lactams, are already resistant to them, and they can become resistant during treatment, which can make the treatment fail. P. aeruginosa isolates from ICU patients who had Per-1 and VEB-1 were the main focus of this study. These two ESBLs are the two most common in ICU patients who had them. 50 isolates were gathered from Peshawar's LRH ICU facilities in the year 2021. The antibiotic susceptibility test was conducted in accordance with the Clinical and Laboratory Standards Institute's ...


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